There is a game ending glitch in The Legend of Zelda: Skyward Sword. This game ending glitch results when you are on the quest to collect the Song of the Hero. It triggers by several events which are listed below:

• Heading to Lanayru Desert and collect the Song of the Thunder Dragon before collecting the Song of the Water and Fire Dragons.
• Head to Lanayru Mine and speak to Golo the Goron.
• Complete the side quest to get the Song of the Thunder Dragon.
• Speak to Golo the Goron again before reaching Faron Woods and Eldin Volcano.
• Now it is impossible for Link to gain the other two songs due to the events not activating again.

In order to bypass this bug, collect the Song of the Water/Fire Dragon before you continue and do not speak to Golo the Goron in Lanayru Mine. If you have encountered this glitch and cannot proceed, send your Wii in and whatever file your Skyward Sword game is in to Nintendo and they will patch it up.

Edit as of 12/21/11: You can now also download a Wii Channel and follow the on screen instructions to fix your Skyward Sword game.